巨菌草幼叶及根转录组功能基因测序及分析

doi:10.11686/cyxb2020326

摘要/Abstract

摘要：

巨菌草生物量巨大，根系发达，是一种理想的水土保持、防风固沙禾本科C₄植物。为了探讨巨菌草转录组信息，对其幼叶、根样本进行Illumina高通量测序和差异表达基因分析。经组装拼接共获得210806个转录本（transcripts）和150336条单基因簇（unigene），平均长度分别为760和642 bp。将获得的unigene与通用公共数据库进行比对，共有88765条unigene获得了基因注释。通过将巨菌草幼叶与根进行比较，共鉴定到5735个差异表达基因（DEGs），其中上调3435个，下调2300个。对DEGs做GO功能分析，上调DEGs主要集中在电子传递，碳水化合物代谢，金属离子结合等过程，下调DEGs则与代谢过程，催化活性，小分子代谢过程等相关。KEGG pathway富集分析共得到120条代谢通路，其中参与光合生物的固碳作用通路DEGs富集程度最高；参与次生代谢物的生物合成通路的DEGs数目最多。对DEGs转录因子分析显示，bHLH和WRKY是调控叶、根差异表达的主要转录因子。研究结果极大地丰富了巨菌草转录组信息，为今后巨菌草分子生物学研究提供了宝贵的数据资源，同时为巨菌草品种改良提供了理论依据。

关键词: 巨菌草, 转录组, 差异表达基因, 转录因子

Abstract:

Giant Juncao （Pennisetum giganteum）is a Poaceous C₄ plant that grows to more than 3 m in height， with high biomass and a well-developed fibrous root system making it ideal for use in waterway， soil and sand stabilization， and as a wind shelter. In order to investigate transcriptome information of Giant Juncao grass， high-throughput Illumina sequencing was conducted on tissues of young leaves and roots， gene expression profiles of leaves and roots were compared， and differentially expressed genes （DEGs） were identified. A total of 210806 transcripts and 150336 unigenes were de novo assembled with an average length of 760 bp and 642 bp， respectively. A total of 88765 unigenes were annotated from at least one of the following databases： Nr， Nt， Swiss-Prot， KOG， GO， KEGG and Pfam. Comparing the young leaf and root tissues， 5735 DEGs were detected， of which 3435 were upregulated and 2300 were downregulated unigenes. GO function analysis showed that upregulated DEGs were mainly involved in electron transport， carbohydrate metabolism， and metal ion binding， while downregulated DEGs included those related to metabolic processes， catalytic activity， and small molecule metabolic processes， among others. KEGG pathway enrichment analysis identified a total of 120 metabolic pathways， among which the DEGs involved in carbon fixation of photosynthetic organisms showed the highest level of enrichment and DEGs involved in biosynthesis of secondary metabolites were the most abundant. Two DEG transcription factors， bHLH and WRKY， were identified as the main regulators of differential gene expression in leaves and roots. This study has greatly enhanced the transcriptomic information available for Giant Juncao， provided a valuable data resource for future molecular biology research， and established a theoretical foundation for improvement of Giant Juncao varieties.

Key words: Giant Juncao, transcriptome, differential expression genes, transcript factors

周晶, 陈思齐, 史文娇, 阳伏林, 林辉, 林占熺. 巨菌草幼叶及根转录组功能基因测序及分析[J]. 草业学报, 2021, 30(2): 143-155.

Jing ZHOU, Si-qi CHEN, Wen-jiao SHI, Fu-lin YANG, Hui LIN, Zhan-xi LIN. Transcriptome analyses of functional genes in young leaves and roots of Giant Juncao[J]. Acta Prataculturae Sinica, 2021, 30(2): 143-155.

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基因 Gene ID	引物 Primers	基因 Gene ID	引物序列 Primers
c104596_g7	S: ATGAGACTGGTATAAGGATGTT A: GAAGCAACTTGGTGTTAGAG	c106511_g1	S: TTGCTGGTTCATTCTCTG A: TTCCTATTGCCATCTCTTG
c100788_g2	S: TGGAATGTGGAATGAGAT A: TAGCAGTTGTAGATTACCT	c97722_g1	S: GTCGCACAACAATCTTCT A: GCATACTATCGGTCTTCATC
c112282_g1	S: CAATCTTGTGACTGAATC A: GATGTTGTAGTTCTGAATC	c106537_g6	S: GACCATCTTACTCTGACT A: CCAACCAATACTTCATCC
c107530_g1	S: AGTTAGTACCAGAGGATA A: AGCATCTATGTTCTTGTA	PgACT	S: TGCTCAGTGGAGGGTCTACCAT A: CAGGTGGTGCAATCACTTTAAT
c99519_g1	S: TACTTCTCCTCTAATGCTTGTG A: GGTAAGGTGCCTATTGTGAA

基因 Gene ID	引物 Primers	基因 Gene ID	引物序列 Primers
c104596_g7	S: ATGAGACTGGTATAAGGATGTT A: GAAGCAACTTGGTGTTAGAG	c106511_g1	S: TTGCTGGTTCATTCTCTG A: TTCCTATTGCCATCTCTTG
c100788_g2	S: TGGAATGTGGAATGAGAT A: TAGCAGTTGTAGATTACCT	c97722_g1	S: GTCGCACAACAATCTTCT A: GCATACTATCGGTCTTCATC
c112282_g1	S: CAATCTTGTGACTGAATC A: GATGTTGTAGTTCTGAATC	c106537_g6	S: GACCATCTTACTCTGACT A: CCAACCAATACTTCATCC
c107530_g1	S: AGTTAGTACCAGAGGATA A: AGCATCTATGTTCTTGTA	PgACT	S: TGCTCAGTGGAGGGTCTACCAT A: CAGGTGGTGCAATCACTTTAAT
c99519_g1	S: TACTTCTCCTCTAATGCTTGTG A: GGTAAGGTGCCTATTGTGAA

核苷酸长度 Nucleotides length	转录本 Transcripts	单基因簇 Unigenes (No.)
<300	67010	59354
300~500	48148	37777
500~1000	45684	28059
1000~2000	34342	16704
>2000	15622	8442
总数Total	210806	150336
最短长度 Shortest length	201	201
中间长度 Median length	444	359
最长长度 Longest length	14723	14723
平均长度 Mean length	760	642
不小于总长 50% N50	1231	995
不小于总长90% N90	297	261

核苷酸长度 Nucleotides length	转录本 Transcripts	单基因簇 Unigenes (No.)
<300	67010	59354
300~500	48148	37777
500~1000	45684	28059
1000~2000	34342	16704
>2000	15622	8442
总数Total	210806	150336
最短长度 Shortest length	201	201
中间长度 Median length	444	359
最长长度 Longest length	14723	14723
平均长度 Mean length	760	642
不小于总长 50% N50	1231	995
不小于总长90% N90	297	261

GO登录号GO accession	功能Function	基因数量Gene number (No.)
GO:0007118	芽生细胞顶端芽生长 Budding cell apical bud growth	2
GO:0048588	细胞生长发育 Developmental cell growth	52
GO:0060560	涉及形态发生的生长发育 Developmental growth involved in morphogenesis	67
GO:0080186	营养生长发育Developmental vegetative growth	3
GO:0044182	单细胞生物种群的丝状生长Filamentous growth of a population of unicellular organisms	48
GO:0035266	分生组织增长Meristem growth	43
GO:0045926	生长负调节Negative regulation of growth	4
GO:0030307	细胞生长的正调控Positive regulation of cell growth	4
GO:0048639	发育生长的正调控Positive regulation of developmental growth	4
GO:0090033	丝状生长的正调控Positive regulation of filamentous growth	2
GO:0045927	生长正调节Positive regulation of growth	10
GO:0007124	假菌丝生长Pseudohyphal growth	3
GO:0001558	细胞生长调节Regulation of cell growth	42
GO:0048638	发育生长调节Regulation of developmental growth	108
GO:0010570	丝状生长的调节Regulation of filamentous growth	8
GO:0040009	生长速度调节Regulation of growth rate	4
GO:0046620	器官生长调节Regulation of organ growth	10
GO:0080112	种子生长Seed growth	1
GO:0009826	一维细胞生长Unidimensional cell growth	33